The Spirit Within
by August08
Summary: A young ninja-in-training is sent on a pilgrimage to a lost and ancient temple to reconnect the world to the spirits that once ruled over the land. Along the way, he meets three unlikely companions that will not only help him in his quest, but help him discover who he is and his place in the world. 2k12 AU.
1. Chapter 1

**A/N** : I should really stop looking at pictures that give me inspiration for stories. I know it's a good idea to listen to your muse, but what are you to do when that muse gives you so many story ideas you don't know what to do with them? Write them out and hope for the best, I guess. This doesn't mean I have abandoned my other stories...far from it. I'm just waiting on my other muses who are in charge of those stories to come back from vacation so I can get working on them again.

So, without further ado, I present to you: The Spirit Within. Hope you enjoy.

 **Disclaimer** : I own nothing.

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We were the guardians of an advanced, ancient race. We guided those under our care with love and patience. We helped them grow, to mature. We gifted them with wisdom, knowledge, courage and hope. They flourished into a vast, cultured people; spreading out to distant lands and establishing themselves as a proud nation. However, like most children, ours grew rebellious. Wars broke out among the different tribes. We tried our best to aid, but we soon felt that we could not take sides.

The wars raged on and we could do nothing more than to dwell in our temple and watch helplessly as the land we worked so hard to provide for our children was lost. Blame for the misfortunes was placed on us. We were accused of not caring about what happened to the people nor the land. The tribes attempted to storm the temple, but we saw them coming and raised our dwelling place high into the mountains where no one would be able to reach it.

But, reach it they did. Those who wished to see us burn for crimes we did not commit reached the temple walls. They stormed the temple, barging into the inner sanctum. They tried to take us, but we would not be taken. We cast ourselves out of that place, disappearing into the wilds of the world. We shed our spiritual bodies and took the forms of mortals.

Now, centuries have passed, but war still plagues the land. We lie in wait for the day when we will be reunited with our true forms. Then, and only then, will we put a stop to the fighting, once and for all.

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I know it's not much to go on, but the following chapters will be much more detailed and a lot longer. So, please bear with me.

Reviews are welcome, flames are not


	2. Chapter 2

**Disclaimer** : see chapter one

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Two young warriors circled each other, hands on the hilts of their swords, eyes locked on the other. One was a white rabbit, the other a blue masked turtle. They were both in their mid-teens, yet they had surpassed everyone else in their classes. This was their final test before moving on to the next stage of their training. Their teacher, a wizened rat by the name of Splinter, watched on alongside the young rabbit's father. Both boys had a look of determination on their faces; knowing that, even though they were friends, only one was going to come out on top.

"Hajime," Splinter commanded.

With that order, there was the singing of steel and then the clash of metal on metal as the swords connected. Splinter watched his students closely. The rabbit, Usagi, was already a fierce fighter at such a young age. The same could be said about the turtle, Leonardo; but, it seemed like something was holding him back. Splinter had tried countless times to get his adopted son to talk to him, but Leonardo just locked himself in his room and would only come out when he needed to. And it was clear that Leonardo was distracted by something, since he wasn't attacking as hard as he usually did. Usagi swung his sword, catching Leonardo across the hands and sending his sword flying. Leonardo stumbled back, panting for breath.

"Yame," Splinter called.

Usagi sheathed his sword and the friends bowed to each other. Leonardo retrieved his own sword and sheathed it before joining Usagi who was now kneeling, waiting for Splinter to speak. Leonardo could see the look of approval in Usagi's father's eyes.

"What do you think, Splinter?" the older rabbit asked. "Is my son ready?"

"He is a skilled warrior, yes. But, I am not sure if he is the right one to send," Splinter replied.

Leonardo and Usagi looked at each other before looking back at their teacher. "To send where, sensei?" Leonardo asked.

"You said whoever wins this fight will be chosen to go to the Spirit's Temple," Usagi's father said.

"The Spirit's Temple?" Usagi repeated in awe.

"I thought that was just a myth," Leonardo said.

Splinter looked at his students. "No, my son. It is a very real place. And whomever we send there cannot be just anyone."

"So, send my son," the rabbit insisted. "He's more than capable."

"It is a very difficult journey through jungles and wilderness and a long passage across the ocean," Splinter explained. "Then, there is the climb up the mountain to get to the temple entrance. Mortal feet have not passed over that threshold in centuries." He looked from the father to the boys. "It will be a journey of self-reflection as well as endurance. It will be hard, with no guarantee that whoever goes will come back." Splinter glanced back at the father. "Do you still wish for your son to be the one to go?"

"I'll go," Leonardo said. Everyone turned to look at him, eyes wide. Leonardo swallowed. "I mean, Usagi has ties here. If he goes and doesn't come back it'll be extremely hard on his family." He looked at Splinter. "I'm not saying I'm ungrateful for all you've done for me, Master Splinter. But...you said this was going to be a journey of self-reflection, and Usagi already knows who he is. But, I don't. I've always wondered where I came from, and maybe this pilgrimage will help me find out who I am and where I came from."

Usagi placed a hand on his friend's shoulder. "You will have my support and my prayers, my friend," he said.

Leonardo smiled. "Thank you, Usagi."

Splinter gave his son a proud look. "If that is what you wish, Leonardo, then you have my blessing," he said.

Leonardo bowed. "Thank you, Master Splinter."

"It will be a long journey. You will have to leave right away," Splinter said.

Leonardo got to his feet and hurried away. The others watched him disappear out of the dojo. Usagi's father turned to Splinter.

"Do you think he knows?" he asked. "Somewhere deep inside, I'm sure he's felt it."

"This journey will decide everything," Splinter replied. He felt his heart sink a little bit. "If he fails, then there is no telling what horrors await us in the future."

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Leonardo shifted the sheaths of his swords on his back so that it was more comfortable. He looked down at his pack, knowing that everything he was going to need for the next few weeks, or even months, lay inside. Leonardo glanced up when he heard footsteps coming towards him. Splinter walked up, looking proud and holding a small bundle in his hands.

"What's that?" Leonardo asked, pointing to the bundle.

Splinter held it out and unwrapped the cloth, revealing three items. One was a golden ring that opened up in front into a simple swirl design, making it look like a crown. The second was a bracelet made out of beads, and the third was a necklace that was also made out of beads.

"These are some items that may help you on your journey," Splinter explained.

"How?" Leonardo asked in confusion.

Splinter placed the package in his son's hands. "You will know when the time is right," he said cryptically.

Leonardo shrugged, folding up the cloth again and placed the bundle in his pack. He turned around and gave Splinter a hug.

"Thanks for everything, sensei," he said.

Splinter held his son close. "Good luck, Leonardo. May the spirits watch over and guide your journey."

Leonardo broke away and picked up his pack. "See you when I get back," he said.

He shouldered the pack and started off towards the village gates. When the gates were in sight, Leonardo felt his heart begin to race. As soon as he stepped across that threshold he was on his own. The young warrior took a deep breath, and without looking back, passed under the gate.

It was a strange new world for him, but Leonardo was determined to find his place in it.

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Reviews are welcome, flames are not


	3. Chapter 3

**A/N** : Yay for midnight writing moods. Better than midnight snacks :D Thanks to everyone who has read and reviewed thus far. I'm glad you're enjoying the story.

 **Disclaimer** : see chapter one

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Rain poured from the heavens, pelting the young turtle as he slowly trekked through the jungle. His stomach growled in hunger, but it was pointless to try to build a fire in the middle of a rain storm. He had other things to eat that didn't require cooking, but he wasn't in the mood for raw food. Leonardo pulled the hood of his cloak tighter around his head, trying to keep as much of the rain off of him as he could. He was already missing his warm bed back at the dojo. He missed Usagi, he missed Splinter. He missed his home. But, he had volunteered for this mission. He had been told it was going to be hard and he took it anyway.

 _Stop whining and pick up the pace,_ Leonardo told himself.

A noise in the trees made the turtle stop and look up; heart jumping up in his throat. His blue eyes instantly locked gazes with deep, emerald green eyes. Leonardo blinked in surprise when he realized he was staring up at a small monkey. Its fur was an unusual dark shade of red. The little creature tilted its head to one side in a quizzing manner.

"Hey, little guy," Leonardo said.

The monkey wrapped its tail around the branch it was on and hung upside down, its eyes never leaving the strange two legged turtle with the blue eyes. Leonardo slowly bent down, shrugging out of the straps of the backpack. He opened the pack and took out a small packet of food.

"You hungry? I know I am," Leonardo said.

He unwrapped the cloth and found some cheese and bread. The monkey sniffed the air and fell down to the ground as Leonardo sat down on a tree root. The turtle tore off a small piece of bread and held it out in his palm. The monkey ventured up to the outstretched hand, sniffed at the strange food before snatching the bread away. Leonardo smiled as he watched the little creature nibble away at the bread. He picked up a piece of cheese and nibbled at it. When the monkey was done with the bread, it looked up at Leonardo expectantly; licking its lips.

Leonardo popped the rest of the cheese into his mouth and broke off another piece of bread. The monkey took the offering and began eating again. Leonardo sat back against the tree, watching the little creature. Something about it seemed familiar, but he didn't know why. It was the first sign of life he had seen since leaving the safety of the village; and Leonardo hoped that it would be the only sign.

"Hey!" he suddenly yelled when the monkey grabbed the last of the bread and cheese while he was distracted with his thoughts.

Leonardo growled in annoyance as the monkey scurried away, hiding in a tree where the funny looking turtle couldn't reach it. The little creature made a noise that sounded suspiciously like laughter. Leonardo glared up at the monkey who grinned back before shoving a chunk of cheese into its mouth. Leonardo tucked the empty cloth back into his pack. He wasn't full, but at least the hunger was gone.

"I hope you choke," Leonardo grumbled up at the monkey as he shouldered the pack again.

As if on queue, the monkey made a harsh choking sound; but Leonardo chalked it up to the monkey mocking him. He stalked away, soaking wet and face burning with embarrassment.

 _Out-smarted by a monkey,_ Leonardo inwardly fumed. _At least Usagi wasn't here to see it._

He pulled the cloak tighter around his body, but it did little good to keep the rain and the cold out since it was soaked through. Leonardo knew he was soon going to have to try to find some kind of shelter. As he walked, he could feel someone watching him. There was the rustling of leaves and Leonardo could only guess that the monkey was following him.

 _Probably looking for more food,_ he guessed.

Leonardo looked up into the trees, his eyes falling on a moving ball of red fur. There was something about that monkey. The tiny creature hopped from tree to tree as if leading Leonardo through the jungle. The turtle soon came to a small clearing with ruined huts built around a collapsed fire pit. Grateful that he had some shelter, Leonardo ducked into one of the huts and out of the rain. He set the pack down and peeled off the wet cloak. Leonardo then unhooked the sleeping roll from the top of the pack and laid it out on the ground.

He looked out through the doorway, his eyes falling upon a tall, looming stone temple off in the distance. His hopes rose at the thought that he had found the Spirit's Temple, but they dropped again when he realized that the temple he sought was lost in the mountains; and they were weeks, if not months, away. Leonardo settled into the bed roll and closed his eyes. He took a deep breath; breathing in the scent of wet earth and slowly let it out.

His dreams took him to a far away land where spirits ruled and the land and its people were at peace.

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Leonardo woke up to a bright sunbeam shining in his face. He stirred and moaned in his sleep, not wanting to wake up. Eventually, the sun won and Leonardo opened his eyes to see the jungle outside the hut sparkling with rain water. Colors danced in the sunshine, casting small rainbows. Leonardo sat up and stretched, putting a hand over his mouth to stifle a yawn. He slipped out of the bed roll and got to his feet; stepping out of the hut and basking in the warm sunlight.

The stone temple still looked as foreboding as it did the night before and Leonardo was curious to know what lay inside. He was surprised the little red monkey wasn't around, but figured it had gotten bored with him and went to find some other animal to annoy...hopefully a poisonous reptile. Leonardo was still a bit sore about the little pest stealing his supper last night, but the monkey was just being a monkey and didn't mean any harm; it was probably just as hungry as Leonardo had been.

With the thought of food, Leonardo prepared a satisfying breakfast and ate in peace and quiet. As he ate, Leonardo studied the temple, his curiosity growing with each passing second. It was like a little voice in the back of his mind was calling out to him, telling him to explore the temple. So, after cleaning up from breakfast, Leonardo put on his dry cloak and pulled on the pack before setting out in the direction of the temple.

It took him an hour to reach the clearing that housed the massive structure. Leonardo strained his neck to look upward. It was a haunting place. He could almost feel the presence of people long since passed flowing from the temple opening. Swallowing nervously, Leonardo began the long climb up the high temple steps. By the time he reached the top, his legs and feet were burning. He made a quick sweep of the entrance before stepping inside.

A strange, almost familiar power resonated from the walls; like water seeping through cracks in rock. Leonardo walked through the temple, exploring the various rooms, but seeing nothing spectacular. Then, as he ventured deeper into the temple, Leonardo thought he heard shrieks coming from somewhere deeper within the temple. He followed the sounds and came upon the inner sanctum. He let out an awe-inspired gasp.

The large room was filled from floor to ceiling with monkeys. They were shrieking and screaming, hitting their small hands off of the stone. And in the middle of it all was the little red monkey Leonardo had met the night before. It lay on its stomach, clearly distraught over what was happening. Leonardo could only guess that the poor creature was in some kind of trouble for the leader was shrieking louder than the others combined. He didn't know why, but Leonardo got the feeling that the unfortunate monkey was in trouble for interacting with him.

Leonardo shrugged out of the pack and opened it, pulling out the packet with the three items in it. He picked up the crown shaped object and put the other two back. He then stepped into the room and immediately every monkey inside went deathly silent. The red monkey looked over its shoulder and glanced up at him with big green eyes.

"Uh...hi," Leonardo said, not knowing what else to do. "I know you're all a bit upset with your friend here, but he really didn't mean any harm." The statement earned him a snarl from the leader. "He was just hungry...and curious. Wouldn't any of you be curious to see a two-legged turtle walking through your jungle?" Leonardo asked, inching closer to the middle of the room. "I'm sure you would be. I mean...turtles belong in the ocean, not in the jungle. Your friend was just helping to point me in the right direction."

His talk seemed to be calming the monkeys down. Leonardo reached the middle and knelt down, his eyes never leaving the leader. The red monkey looked from the turtle to the leader, its eyes wide with fright.

"I just came to give this to him," Leonardo said, holding out the crown object. "It's a thank you gift for helping me. I'll just put it on and be off."

However, when the gold touched the red monkey's head, it began to glow. Leonardo fell back in surprise when the monkey's eyes turned solid green and the glow enveloped the creature's body. The other monkeys started shrieking again and took off for the exit. Leonardo, however, was fixed in place as he watched the monkey's body morph into something else. When the light died down, Leonardo found himself staring at another turtle. However, this turtle had some monkey traits; a tail for one thing, and fur around his wrists, ankles and neck for another.

The monkey turned turtle groaned as he sat up and stretched. He looked around in confusion before his eyes landed on the very startled Leonardo. The now red masked turtle gave the blue masked turtle a questioning look.

"What are you looking at?" the monkey turtle asked.

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Reviews are welcome, flames are not


	4. Chapter 4

**A/N** : Written at a more sensible hour of the day and I'm not as tired or sleep deprived, so that's a bonus. Anyway, hope you enjoy chapter four.

 **Disclaimer** : see chapter one

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Leonardo sat frozen in place, staring at the turtle before him. Deep, emerald green eyes looked at him through a dark red mask. Leonardo noticed that there was a chip missing from the turtle's plastron near his left shoulder, but it was slightly hidden by the fur around his neck. The monkey turtle's tail twitched in annoyance and he growled under his breath.

"Hey! Blue boy, snap out of it," the monkey turtle snapped.

Leonardo blinked and met his gaze. "Sorry," he apologized. "I just wasn't expecting _that_ to happen."

The monkey turtle touched the crown. "Neither was I. But, thanks for getting me out of trouble," he said.

"No problem," Leonardo replied. "So, uh...what's your name?"

"Raphael," the monkey turtle answered.

Leonardo gave him a questioning look. "Raphael? What kind of a name is that for a monkey?"

"Oh yeah? What's _your_ name, then?" Raphael asked.

"Leonardo," Leonardo replied.

"What kind of a name is _that_ for a _turtle_?" Raphael wanted to know.

Leonardo felt his face begin to burn from embarrassment. "I think I liked you better as a monkey," he commented as he got to his feet.

He left the room, picked up the pack and made his way out of the temple. As he started down the stairs, Leonardo got the feeling that someone was behind him. He turned around but didn't see anyone. Shrugging, Leonardo continued on his journey. He trekked through the jungle for a half hour before the feeling of being watched came over him again. Leonardo turned around, this time catching sight of Raphael a little ways away.

"Are you following me?" Leonardo called.

"No," Raphael called back. "You're just going in the same direction I am."

"Uh huh," Leonardo muttered.

He turned around and continued walking. A minute later, a little red monkey shot through the trees. Leonardo stopped and watched in curiosity. The monkey wore the crown he had given Raphael.

"So, you can shift between two forms, now?" Leonardo asked.

Raphael made a strange sound which Leonardo took to mean, "What of it?"

"Just trying to make conversation," Leonardo said. "Though I have no idea why I'm talking to a monkey for such a thing."

Raphael jumped out of the tree, transforming back into a turtle in mid-air. He landed in a graceful crouch before falling into pace with Leonardo.

"Better?" Raphael asked.

Leonardo shrugged. "I guess."

"Monkey or turtle? Which one do you want?" Raphael snapped.

"Bit of a hot tempered primate, aren't you?" Leonardo asked.

"You would be, too if you were going to be fed to the river monster," Raphael said.

Leonardo frowned in confusion. "River monster?" he repeated.

Raphael shuddered. "A leathery giant with sharp teeth," he replied.

"I would like to see this so-called monster," Leonardo said.

Raphael looked at him with wide eyes. "Is the heat getting to your brain? No one goes to the river. Not unless they have a death wish."

"What's the matter, Raphael? Scared?" Leonardo teased.

Raphael huffed in annoyance. "Fine," he grumbled. "Keep up if you can."

He jumped for a nearby tree, transforming into his monkey form before he grabbed a branch. Leonardo had to run to keep up with him. The little guy was fast. Raphael leapt from tree to tree, not bothering to look back to see if Leonardo was still behind him. Soon, the trees parted, leading out to a small sandy shore that gave way to a wide river. Leonardo broke through the trees, panting for breath. He looked up to see Raphael hanging upside down from a tree branch. The monkey had a smug look on his face.

Leonardo dropped the pack and walked out to the water's edge. He looked down into the fast flowing water. There was no sign of any monster. Leonardo put the tip of his toes into the water. It was warm to the touch. Leonardo put his foot into the water and when nothing happened, he waded out into the river where the current wasn't so strong. Raphael watched from his branch. The turtle was crazy.

Then, he saw it. A long shadow slowly making its way towards where Leonardo was swimming. Raphael let out a shriek of warning. Leonardo turned to look at him but his attention was drawn away by something that brushed up against his leg. He looked down to see two glowing white eyes staring up at him from the murky depths. Leonardo jumped back as a massive crocodile sprang from the water. The beast roared in anger. It turned its solid white eyes to the small turtle, baring razor sharp teeth.

"You dare to defile the Spirit's River?" the crocodile snarled.

For the second time that day, Leonardo was frozen in place. The beast lunged towards him. Leonardo closed his eyes, waiting for the end. However, there was a shriek and a roar. Leonardo opened his eyes to see Raphael clawing at the beast's eyes in a fit of unholy fury. The larger animal shook its head, trying to dislodge the monkey. Leonardo got to his feet and scrambled away as the crocodile stepped where he had been sitting. The beast managed to grab Raphael, tearing him away from its face and plunged the tiny creature into the water, holding him down. Raphael began to struggle, clawing at the beast's hand.

"Stop," Leonardo gasped. He took a breath. "Stop!" he screamed.

The beast shot its gaze towards him, its eyes growing wide. The animal suddenly pulled back, releasing Raphael. Leonardo ran forward and scooped his new friend up out of the water. Raphael coughed and gasped for air. Leonardo rubbed Raphael's back until he was able to get a calming breath.

"Forgive me," the crocodile apologized, its eyes losing its solid color to be replaced by dark brown eyes. "I have been the guardian of this river for many millennia. It was a gift to the desert dwellers by the spirits."

"What's your name?" Leonardo asked.

Raphael looked up at him in surprise. The look said, "He tried to kill me and you're asking his name?"

"My name is Leatherhead. It was a name given to me by one of the spirits themselves."

"I'm Leonardo. And, this is Raphael," Leonardo said. "Why did you look so scared when I yelled?"

"You sounded like an old friend," the crocodile replied. "Someone I knew many moons ago." He looked down at Raphael, who glared back up. "You are gifted to have such a brave warrior as a friend," Leatherhead said. "Forgive me, little one."

Raphael let out a hiss and scampered up Leonardo's arm to rest on the turtle's shoulders. Leonardo shook his head.

"No harm done," the blue masked turtle said. "All is forgiven."

Leatherhead bowed his head. "Thank you, my friend."

Leonardo smiled. "Well, I guess we'd better get going. That temple isn't going to find itself."

Leatherhead raised his head in surprise. "What temple?" he asked.

"The Spirit's Temple," Leonardo replied. "The one that was lost in the mountains."

Leatherhead took a deep, sharp breath. "The time has finally come," he murmured.

Leonardo and Raphael looked at each other before turning back to Leatherhead. "The time for what?" Leonardo asked.

"You will find out in due time," Leatherhead told him, stepping backwards towards the river. "For now, farewell and safe journey."

Leonardo waved as Leatherhead disappeared under the water. Raphael let out another hiss before leaping off of Leonardo's shoulders and scurrying away from the river. Leonardo followed him, picking up his pack as he went and shouldered it. There was a lot of ground to cover and there was no telling what waited for them in-between.

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Reviews are welcome, flames are not


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